Where one study disagrees with what other studies report for the same models, and what we are doing to resolve each case.
These are automatic leads, not findings of error. Each release, a check compares how every study ranks the models it shares with other studies. It flags a study that reverses the order the others agree on, or whose gap to a shared reference model lies well outside theirs. Different tasks, populations or metrics often explain a flag.
A flag never hides a result. Flagged results stay in every table, page and download, marked Contested. A result is withheld only when a reviewer marks it disputed.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks FATHMM-XF above CADD in 10 of 10 comparisons; 2 of 2 other studies rank CADD above FATHMM-XF.
2 papers rank CADD above FATHMM-XF in all 12 comparisons that are not ties (1 is a tie). Comprehensive assessment… ranks FATHMM-XF above CADD in all 10 of its comparisons.
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) ranks CADD above ESM-2 in 14 of 14 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks ESM-2 above CADD in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-2 above CADD in 6 of their 21 comparisons and CADD higher in 15. Of those papers, Genome modelling and design across all… ranks CADD higher on its own (14 of 14).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks CADD above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above CADD in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above CADD in 7 of their 12 comparisons and CADD higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks CADD higher on its own (4 of 5).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above CADD in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks CADD above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank CADD above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).